fastq-tools
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dcjones
Small utilities for working with fastq sequence files.
The documentation link does not exist (raise 404 error on 2022/4/15): https://homes.cs.washington.edu/~dcjones/fastq-tools/
fastq-sample -s 11 -n 3000000 '/home/huilin_hu/Assemble/fasta/Triticum_aestivum_paragon.EIv1.1.dna_sm.toplevel.fa.gz' -o test1.3M.fq hi, hello, I don’t know why the output of the above command is a binary file, is there a solution?
Hi, It would be useful if fastq-sort could remove the temporary files it creates. ``` char const *tmpfolder = getenv("TMPDIR"); if (tmpfolder == NULL) tmpfolder = "/tmp"; ``` The only...
If I attempt to set a custom `$TMPDIR`, `fastq-sort` will ignore it and continue putting files into `/tmp`.
Even though the help page indicates that `fastq-sort -N` and `fastq-sort --idn` are the same, `-N` doesn't seem to work: ```bash $ fastq-sort -N fastq-sort: invalid option -- 'N' ```
I'm building an EasyBuild module for fastq-tools. Compilation fails because a spurious linker option is used: ``` == 2016-05-08 08:08:13,937 build_log.py:152 ERROR cmd " make -j 4 LIBTOOL=libtool" exited with...
This line will cause problems if `LIBS` is already defined because it just adds the option regardless of what `LIBS` currently i:s https://github.com/dcjones/fastq-tools/blob/79dbc8cfa972e5a60381288d86df6571a1b00b1b/configure.ac#L56 See also https://github.com/easybuilders/easybuild-easyconfigs/pull/5396.
Make installation a bit easier for newbies. The lines $ sudo apt-get install libpcre3-dev $ sudo apt-get install zlibc quickly tell how to install the required dependencies. The line $...
